On-lattice agent-based simulation of populations of cells within the open-source Chaste framework
KAUST Grant NumberKUK-013-04
Online Publication Date2013-02-21
Print Publication Date2013-02-21
Permanent link to this recordhttp://hdl.handle.net/10754/599073
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AbstractOver the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors; and ordinary differential equations for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here, we report on the creation of an agent-based multi-scale environment amalgamating the characteristics of these models within a Virtual Physiological Human (VPH) Exemplar Project. This project enables reuse, integration, expansion and sharing of the model and relevant data. The agent-based and reaction-diffusion parts of the multi-scale model have been implemented and are available for download as part of the latest public release of Chaste (Cancer, Heart and Soft Tissue Environment; http://www.cs.ox.ac.uk/chaste/), part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the 'what if' scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia (low oxygen levels). We conclude our work by summarizing the future steps for the expansion of the current system.
CitationFigueredo GP, Joshi TV, Osborne JM, Byrne HM, Owen MR (2013) On-lattice agent-based simulation of populations of cells within the open-source Chaste framework. Interface Focus 3: 20120081–20120081. Available: http://dx.doi.org/10.1098/rsfs.2012.0081.
SponsorsThe research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under the project 'Virtual Physiological Human Network of Excellence', grant agreement no. 223920. This work was also supported in part by award no. KUK-013-04, made by the King Abdullah University of Science and Technology (KAUST).
PublisherThe Royal Society
PubMed Central IDPMC3638480
CollectionsPublications Acknowledging KAUST Support
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